"We've always been a company that's about food — real food, real ingredients, real cooking — and people, making sure that we hire great people, invest in them so that they can run great restaurants," CFO Jack Hartung told "Mad Money" host in a joint interview with Niccol.

"We got knocked on our heels a little bit, so we stopped talking about the things that made Chipotle special," Hartung admitted. "The great thing now, ... since Brian joined and we brought a new team together, is we're back on our front foot. We're talking about our food."

Niccol echoed Hartung's remarks, saying that what he was most impressed with when he joined the fast-casual chain was Chipotle's "commitment to food safety."

But that commitment requires higher standards than companies like Taco Bell, Niccol's former stomping grounds, the new CEO said.

"What we definitely are committed to doing is real ingredients, truly fresh, and that does require different food safety standards to be in place," Niccol told Cramer.

"These wellness checks that we do and other protocols that we execute — you're not going to find that in a lot of other restaurants because we are handling fresh food and we're truly cooking every day in our restaurants," the CEO continued. "So it just demands that we have a higher level of commitment to food safety and we'll always have to be passionate about being a leader in that space."

"We have world-class people on our food safety council and food safety's going to be something that's always going to be a high priority for us," Hartung said. "That's not going to change."

Chipotle's stock ended Thursday trading higher, up 2.60 percent at $447.77 a share. In June, CNBC reported on Niccol's plans to turn Chipotle around and bring it back into favor with customers — read more about his plans here.